Camelia, the Perl 6 bug

IRC log for #bioclipse, 2009-03-19

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All times shown according to UTC.

Time Nick Message
06:08 egonw joined #bioclipse
06:34 egonw joined #bioclipse
07:40 Gpox joined #bioclipse
08:26 masak joined #bioclipse
08:34 egonw joined #bioclipse
08:37 olass joined #bioclipse
08:37 egonw olass: car 'accu' problems... need to go to Renault bilshop...
08:37 egonw will be offline for a while
08:38 olass ok
08:38 olass good luck
08:40 masak 'accu'?
08:41 olass no idea
08:41 olass maybe a dutch word
08:43 masak olass: indeed. 'accumulator'.
08:43 masak olass++
08:43 masak battery.
08:45 olass ah
08:45 olass wonder how they got to the Renault shop...
08:45 olass bus?
08:45 de__maas joined #bioclipse
08:47 masak maybe the car isn't entirely broken down, just malfunctioning.
09:02 CIA-58 bioclipse: goglepox * r9396 /bioclipse2/trunk/plugins/net.bioclipse​.cdk.jchempaint/src/net/bioclipse/cdk/j​chempaint/editor/JChemPaintEditor.java: Update selection when right-clicking for popupmenu fixes bug #662
09:02 zarah bug #662 | http://tinyurl.com/dgfhsy
09:08 * olass hears jonalv through the wall
09:11 jonalv joined #bioclipse
09:13 shk3 joined #bioclipse
09:13 olass hi jonalv
09:14 jonalv hi olass
09:14 olass how is the hand?
09:14 olass better?
09:14 * jonalv is reading shk3s mail. trying to understand it...
09:14 jonalv olass: yes it's better
09:14 jonalv olass: almost good actually. _almost_
09:14 masak .oO( "talk to the hand" )
09:15 olass hey, hands off!
09:15 olass can I give you a hand?
09:15 masak how handy.
09:15 olass just hand it to me
09:16 masak now, this is getting out of hand...
09:16 olass marvellous backhand!
09:16 masak what? :)
09:16 olass so, you canät handle this?
09:16 olass can't
09:16 masak you're not seeing the issue at hand...
09:17 * jonalv throws his hands up in the air likes he just don't care and dives back into shk3s mail
09:17 olass yes, feeling sort of handicapped
09:17 masak I've gotta hand it to jonalv. he's handling this extremely well.
09:18 olass do that. I feel like I'm wearing handcuffs
09:24 CIA-58 bioclipse: jonalv * r9397 /bioclipse2/trunk/plugins/net.bioclipse.u​i/src/net/bioclipse/ui/Application.java: squuesed class into 80 cols and added a little bit more info to printing of exception
09:32 shk3 hi
09:32 zarah privet shk3
09:32 shk3 hope I didn't confuse you too much
10:13 shk3 so what do you think?
10:16 de__maas left #bioclipse
10:28 CIA-58 bioclipse: ospjuth * r9398 /bioclipse2/trunk/features/net.bioclips​e.chemoinformatics_feature/feature.xml: Updated versionins after beta4 release.
10:29 CIA-58 bioclipse: ospjuth * r9399 /bioclipse2/trunk/plugins/net.b​ioclipse.ui/bioclipse.product: Updated versionins after beta4 release.
10:37 thomas_ku joined #bioclipse
10:44 CIA-58 bioclipse: jonalv * r9400 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/META-INF/MANIFEST.MF: removed version specification
11:20 egonw joined #bioclipse
11:41 jonalv egonw: oh hai
11:42 egonw hi jonalv
11:42 CIA-58 bioclipse: carl_masak * r9401 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/IUIManager.java:
11:42 CIA-58 bioclipse: [IUImanager] removed @Published annotation
11:42 CIA-58 bioclipse: Removed @Published annotation on open(IBioObject, String)
11:45 * jonalv lunch
12:41 egonw sunbird++
12:42 jonalv songbird++
12:43 jonalv zarah: ping
12:43 zarah jonalv: pong
13:03 CIA-58 bioclipse: egonw * r9402 /bioclipse2/trunk/plugins/net​.bioclipse.data.blueobelisk/ (build.properties doc/ doc/index.html plugin.xml toc.xml): Added missing licenses (fixes #714)
13:03 zarah bug #714 | http://tinyurl.com/dma337
13:04 olass joined #bioclipse
13:07 CIA-58 bioclipse: egonw * r9403 /bioclipse2/trunk/plugins/net​.bioclipse.data.blueobelisk/ (META-INF/MANIFEST.MF build.properties): Added itself to the classpath
13:14 CIA-58 bioclipse: carl_masak * r9404 /bioclipse2/trunk/plugins/net.bioclipse.ui.busine​ss/src/net/bioclipse/ui/business/UIManager.java: [UIManager] removed unused imports
13:18 egonw olass: can you glance at bug #374?
13:18 egonw and veto/approve?
13:18 egonw @pz 374
13:18 zarah http://pele.farmbio.uu.se/cgi-b​in/bugzilla/show_bug.cgi?id=374
13:19 olass mom
13:20 olass egonw: why does net.bioclipse.cheminformatics depend on cdk? That was not the intention...
13:20 olass it was supposed to be the other way around
13:20 egonw mom, I'll chek
13:20 egonw +c
13:20 olass In retrospect... it cannot go into net.bioclipse.cheminformatics, because the
13:20 olass latter depends on CDK, resulting in circular deps. So, reopened.
13:21 egonw btw, where's the test data?
13:21 olass test data in what context?
13:21 olass sample data?
13:21 egonw yeah, maybe...
13:21 egonw ok
13:21 olass hmm hmm
13:21 olass I see what you mean
13:22 olass content types require cdk?
13:22 olass is that so?
13:22 egonw no
13:22 olass hmm
13:22 egonw there is import of the ICDKManager
13:22 egonw checking out why
13:23 olass teh reason for having the net.bc.cheminfo plugin was to have a plugin that was NOT dependent on cdk
13:23 egonw shk3: ping
13:23 olass MoleculeFileContentProvider seems to require it
13:23 shk3 hi egonw
13:23 olass who placed that there???
13:24 egonw shk3: does the MoleculeFileContentProvider need the ICDKManager?
13:24 olass and why?
13:24 shk3 I suppose so
13:24 shk3 would need to look
13:24 olass if require cdk, place it in cdk
13:24 shk3 I remember I discussed that with you
13:24 olass and please remove cdk dep in net.bc.cheminfo
13:24 egonw shk3: it seems that is no longer needed
13:25 egonw shk3: as it now uses content types...
13:25 egonw and not file extensions
13:25 shk3 indeed
13:25 egonw cheers for removal of file extensions!
13:25 shk3 not needed
13:25 egonw OK, will remove it...
13:25 egonw it does not give compile errors it seems
13:25 olass egonw++
13:25 olass and then content types can go there
13:25 olass it seems like the logical place
13:26 shk3 looks good without cdk
13:26 olass all cheminfo that is independent of an implementation should go there
13:26 shk3 egonw: how can I browse the cdk-1.2.x branch in git?
13:26 shk3 on sf?
13:27 egonw click the branch icon down the bottom of the page
13:27 CIA-58 bioclipse: egonw * r9405 /bioclipse2/trunk/plugins/net​.bioclipse.chemoinformatics/ (2 files in 2 dirs): Removed obsolete dependency on cdk.business
13:28 CIA-58 bioclipse: ospjuth * r9406 /bioclipse2/trunk/plugins/​net.bioclipse.ui/book.css: Added default css for help system. Much nicer now.
13:30 egonw gitk++
13:30 egonw I can filter all commits very fast on committer :)
13:38 egonw masak: ping
13:38 masak egonw: pong.
13:38 egonw masak: you have perl script to create docs for the manager, correct?
13:38 masak aye. it's in the repo.
13:38 egonw can it be called standalone?
13:38 masak as opposed to...?
13:38 egonw or is it only integrated with make website?
13:39 egonw that script BC1 had...
13:39 masak no, it outputs HTML to STDOUT.
13:39 masak very primitive, just as I like it. :)
13:39 egonw OK
13:40 masak egonw: when I update the page on pele, I simply pipe to file, and scp the file.
13:40 egonw can I ask you to make it work in a plugin setting?
13:40 egonw I'll set something up, and ask you to fill in the details...
13:40 masak egonw: sure, if you explain what that means.
13:40 egonw ok, deal
13:41 masak setting up and asking to fill in details works too.
13:52 olass egonw: are InChI in any way dependent on implementation?
13:52 olass do I need to say what version of InChI I used?
13:52 olass implementation I mean...
13:53 egonw no, that's already in the inchi
13:53 olass ok good
13:53 egonw InChI=1/ is version 1
13:53 egonw 1S is Standard InChI
13:53 egonw (which we do not have yet)
13:53 olass ok
13:53 olass when will we get that?
13:54 egonw when Sam updates his InChI library, or we figure out how to patch it
13:56 olass send him an email?
13:57 egonw no, let's not do that...
13:57 olass :)
13:57 egonw 1S is not so important
13:57 egonw and just making a patch is better
13:57 egonw and then email and ask for inclusion
13:58 olass egonw: what is jabref?
13:58 olass and why is that in plugin bibtex?
13:58 egonw bibtex editor
13:58 egonw used for the data model
13:58 olass aha
13:58 olass ok
13:58 egonw yes, should be in a separate plugin
13:58 * olass will do an EMF model from bibtexml schema
13:58 egonw I hold the position that all third party libraries should be in separate plugins
13:59 olass that calls for another plugin I think
13:59 egonw olass++
13:59 olass will try at least
13:59 egonw shk3: would be rather interesting for Speclipse too!
13:59 olass if not works out of the box, It probably stops there
13:59 olass we'll see :)
13:59 egonw ack
13:59 olass anyway, will be a separate plugin
13:59 egonw feel free to let me know error messages...
13:59 olass sure sure
14:00 olass who knows, it might actually work ;)
14:01 olass no, it didn't
14:03 olass egonw: line 156: DescriptionPathResourceLocationType
14:03 olass src-resolve: Cannot resolve the name 'bibtex:BibTeXML.common.fields.class' to a(n) 'group' component.net.bioclipse.bibtexml/​modelbibtexmlHandwritten.xsdline 156XML Schema Problem
14:04 olass src-resolve: Cannot resolve the name 'bibtex:BibTeXML.common.fields.class' to a(n) 'group' component.
14:04 olass the last one is the error message
14:04 olass I get 15 of them
14:04 olass but almost the same all
14:04 egonw ok...
14:05 egonw mom
14:08 egonw confirmed
14:08 egonw the WST XML Schema editor gives these errors too...
14:08 egonw hang on...
14:08 egonw will try to fix that
14:10 CIA-58 bioclipse: egonw * r9407 /bioclipse2/trunk/plugins/ (2 files in 2 dirs): Moved cheminfo content types to the cheminfo plugin.xml (fixes #374)
14:10 zarah bug #374 | http://tinyurl.com/cbl2j9
14:10 egonw oh crap...
14:10 egonw that was not supposed to be commited yet
14:10 CIA-58 bioclipse: egonw * r9408 /bioclipse2/trunk/plugins/n​et.bioclipse.bibtex/schema/ (. bibtexmlHandwritten.xsd): Added broken BibTeXML editor
14:10 egonw the next one is...
14:10 masak with great git comes great responsibility...
14:10 egonw using git branches++
14:10 egonw egonw--
14:11 egonw (for not using branches enough)
14:15 jonalv joined #bioclipse
14:17 jonalv hm egonw now I am banned from the jmol dev list.
14:18 jonalv is that what happends if one turns up there and asks about SVN tags? :)
14:18 egonw no, not banned
14:18 egonw first email was from your sf account
14:18 egonw reply was via gmail
14:19 egonw with which you are not signed up
14:19 jonalv oh I see
14:19 egonw mom
14:19 jonalv how confusing...
14:20 egonw I think someone already approved your post
14:20 jonalv hm
14:20 * jonalv i snot having a great day...
14:20 jonalv the mac refuses to upgrade...
14:22 egonw olass: please try with the next patch
14:22 CIA-58 bioclipse: egonw * r9409 /bioclipse2/trunk/plugins/net.bioclipse​.bibtex/schema/bibtexmlHandwritten.xsd: XML Schema fixes; the WST editor is now happy about it... have not tested EMF...
14:24 olass ok
14:24 olass if the eclipse XSD editor likes it it should work
14:25 egonw only problem is that I am not entirely sure how the broken XML schema was supposed to work
14:25 egonw so made an educated guess
14:25 egonw but this may lead to a conceptually broken model...
14:25 egonw but I can see that from the EMF-created model
14:25 olass works liek a charm
14:25 olass like
14:26 olass committing for your review
14:26 olass slow slow sf...
14:27 CIA-58 bioclipse: ospjuth * r9410 /bioclipse2/trunk/plugins/net.bioclipse.bibtexml/: Initial import.
14:30 CIA-58 bioclipse: ospjuth * r9411 /bioclipse2/trunk/plugins/net.bioclipse.bibtexml/ (64 files in 9 dirs): Added generated EMF model
14:30 olass egonw: please update and review now if you like
14:31 olass will make a simple test case
14:31 egonw ok, hang on
14:32 CIA-58 bioclipse: egonw * r9412 /bioclipse2/trunk/plugins/ (2 files in 2 dirs):
14:32 CIA-58 bioclipse: Revert "Moved cheminfo content types to the cheminfo plugin.xml (fixes #374)"
14:32 CIA-58 bioclipse: Now, because the CML content types actually have to go into net.bioclipse.cml.
14:32 CIA-58 bioclipse: This reverts commit 2fb479aad3fc85a0f24e0ce2b7549cc158c34b53.
14:32 zarah bug #374 | http://tinyurl.com/cbl2j9
14:46 egonw olass: looks good, I think
14:46 egonw checked Article...
14:46 egonw only DOI is missing...
14:46 egonw see next commit:
14:46 olass ok
14:46 * olass is writing a test
14:46 CIA-58 bioclipse: egonw * r9413 /bioclipse2/trunk/plugins/net.bioclipse.​bibtexml/model/bibtexmlHandwritten.xsd: Added missing DOI
14:51 olass anyone who knows how to work with XMLGregorianCalendar?
14:52 * masak 's fix to a new problem served only to reintroduce an old problem
14:52 masak :/
14:52 egonw olass: nope
14:52 egonw olass: not me
14:52 olass ok
14:52 * olass is asking google
14:52 jonalv my git svn is searching aggresively :)
14:53 masak raaawr!
15:12 CIA-58 bioclipse: egonw * r9414 /bioclipse2/trunk/plugins/ (16 files in 11 dirs): Moved CML content types to net.bioclipse.cml; removed jar net.bioclipse.ui/jar/xpp3-1.1.4c.jar (which was on org.xmlpull.xpp anyway)
15:14 olass egonw: does the bibtexml not support URL?
15:14 olass cannot do article.setURL("")
15:15 egonw then we add this
15:15 egonw check the DOI patch
15:15 olass doing that now
15:16 olass hmm, that patch crashed eclipse
15:17 olass what did you do ;)
15:18 egonw what?
15:18 egonw here it was fine...
15:18 egonw which patch?
15:24 masak Jmol makes me happy.
15:25 egonw :)
15:25 olass egonw: dod you add doi to articleType?
15:26 olass cannot see it here...
15:26 olass neither URL
15:26 masak jonalv: dod you welsh cwlmq?
15:26 olass egonw: cannot see URL in schema either
15:27 olass did you commit it?
15:27 jonalv masak: dod you add welsh daddie?
15:27 masak jonalv: cwlmq!
15:27 olass zarah: slap masak and jonalv
15:27 * zarah loves masak and jonalv, so no slapping
15:27 masak :)
15:27 jonalv :)
15:27 jonalv zarah++
15:27 olass @botsmack
15:28 jonalv @botbeer
15:28 zarah ;)
15:28 masak zarah: slap olass
15:28 zarah stop telling me what to do
15:28 olass egonw: around?
15:28 egonw pong
15:28 egonw no, I did not commit
15:28 egonw was a trivial task, I thought you could do that yourself...
15:28 egonw bwahahaha
15:29 olass ah
15:29 olass sure
15:29 olass can we just edit this schema?
15:29 CIA-58 bioclipse: egonw * r9415 /bioclipse2/trunk/plugins/ (6 files in 5 dirs): Moved other cheminfo content types from net.bioclipse.ui to net.bioclipse.chemoinformatics (fixes #374, now for real)
15:29 zarah bug #374 | http://tinyurl.com/cbl2j9
15:29 egonw olass: sure, who cares
15:29 olass ok, thought it was standardized
15:29 egonw we will have patches upstream
15:29 egonw s/have/file/
15:29 olass sort of thought that was the point of it...
15:29 olass to use something standardized
15:29 egonw well, sort of...
15:30 egonw I think URL and DOI are actually part of the standard...
15:30 egonw but clearly not part of the hand written XML Schema
15:30 olass I sort of starting to think I could have stuck with with my own invention, instead of bibtexml if it is this badly updated...
15:30 olass I mean ,URLs are not a new concept
15:31 olass how is it possible that they forgot it?
15:31 olass whateve...
15:31 olass will add it
15:31 olass but there is no inheritance in this schema
15:31 olass so have to add it manually to loads of places...
15:31 olass grrr
15:31 egonw no, no
15:31 egonw don't think so...
15:31 olass yes, yes
15:32 olass grrrr
15:32 * olass bites the bibtexml schema
15:32 olass *chew* *chew*
15:33 egonw OK, hang on
15:33 egonw will commit something
15:33 olass sure
15:33 * olass will not edit this schema
15:33 olass it needs to be processed the natural way first...
15:34 olass I just swallowed it
15:34 olass :)
15:37 egonw ok, try this patch:
15:37 CIA-58 bioclipse: egonw * r9416 /bioclipse2/trunk/plugins/net.bioclipse.​bibtexml/model/bibtexmlHandwritten.xsd: Added URL; DOI and URL are now part of element list for all classes (I think)
15:37 olass egonw: there is no setEntry in the generated class FileType
15:37 egonw mmm... ok, mom
15:38 olass there is also no PubMedID which is in BibTex
15:38 olass nor ISSN
15:38 egonw no, not part of bibtex
15:38 olass ok
15:38 egonw those are typically all extensions...
15:38 egonw but we can just add them to the schema
15:38 olass ISSN too?
15:39 olass I am happy without them :)
15:41 egonw olass: indeed only FileType.getEntries()
15:41 egonw and no add...
15:41 egonw no idea why...
15:41 olass ok
15:41 olass I can have an entry as root
15:41 shk3 what is release plan for bc2?
15:41 olass see wiki
15:42 shk3 still 23rd?
15:42 olass nah
15:42 olass it's currently unset
15:42 olass waiting for things to get into order
15:42 shk3 ok
15:42 shk3 I will be away from 24th to 1st of April
15:42 olass with JCP and MolTable as major blockers
15:42 olass no worries
15:43 olass me too :)
15:47 jonalv olass: that statuslistener you are adding in jmol. There can be only one of those...
15:48 egonw olass: manually add addEntry?
15:48 olass egonw: I might...
15:48 olass jonalv: ok
15:48 egonw olass: I dunno why EMF decided not to add it
15:48 jonalv olass: I think it's removed by jmol when jmol sets it's statuslistner
15:48 olass jonalv: ok
15:53 * jonalv can't confirm it though because Eclipse refuses to let me add breakpoints in binary code which only has attached source and I don't know how to check out and build that version...
15:55 olass egonw: is it not possible to check out a certain version of jmol?
15:55 egonw sure
15:55 olass have they no branches and no tags?
15:55 olass tell jonalv then
15:55 egonw no recent tags
15:55 olass he's been complaining all day
16:01 olass tada!
16:01 * olass just serialized his first bibtexml
16:02 egonw olass++
16:02 jonalv I don't understand what I can do... olass, egonw if you can help me please do so...
16:02 olass I cannot
16:02 olass egonw?
16:02 egonw jonalv: about what?
16:02 olass checking out the source for the jmol jar in our SVN
16:02 jonalv I am trying to debug Jmol to find out what's going on.
16:03 egonw what's the problem with checking out the source?
16:03 egonw jonalv: you've done that before? svn co ?
16:03 egonw or, maybe the source dist on SF?
16:03 jonalv But I can't use the attached source because Eclispe doesn't actually do debug in the binary files and I haven't managed to check out the source...
16:03 CIA-58 bioclipse: egonw * r9417 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added method to fragmentate a ICDKMolecule into atomcontainers (fixes #658)
16:03 zarah bug #658 | http://tinyurl.com/d76r32
16:04 jonalv egonw: there are no tags in the svn repo. Impossible to find the right version as far as I understand...
16:04 olass can you use a date?
16:04 egonw jonalv: mom, checking
16:05 jonalv ...and I did a git svn rebase on Jmol btw and it's been chewing on that one for a couple of hours now... Some sort of strange branching going on in that repo it seems...
16:05 CIA-58 bioclipse: carl_masak * r9418 /bioclipse2/trunk/plugins/net.bioclipse​.scripting.ui/src/net/bioclipse/scripti​ng/ui/views/ScriptingConsoleView.java: [ScriptingConsoleView] more JavaDoc
16:06 CIA-58 bioclipse: carl_masak * r9419 /bioclipse2/trunk/plugins/net.bioclipse.scrip​ting.ui/src/net/bioclipse/scripting/ui/views/ (JsConsoleView.java ScriptingConsoleView.java):
16:06 CIA-58 bioclipse: [JsConsoleView] fixed tab completion on non-things
16:06 CIA-58 bioclipse: Previously, when tab-completing on things that didn't exist, an exception was
16:06 CIA-58 bioclipse: inserted into the input line. Typical non-helpful behavior. Now, an exception
16:06 CIA-58 bioclipse: is logged and a beep is made.
16:06 CIA-58 bioclipse: ospjuth * r9420 /bioclipse2/trunk/plugins/net.bioclipse.bibtexml/ (34 files in 3 dirs): New EMF model with doi and URL
16:08 egonw jonalv: http://jmol.svn.sf.net/viewvc/jmol/branches/v11_6/​Jmol/src/org/jmol/viewer/Jmol.properties?view=log
16:08 zarah egonw's link is also http://tinyurl.com/c2vpkx
16:09 jonalv egonw: hm did I miss that? strange... or did not git svn pick that one up? Will check again when git svn is done...
16:09 CIA-58 bioclipse: ospjuth * r9421 /bioclipse2/trunk/plugins/ne​t.bioclipse.bibtexml.edit/: Initial import.
16:10 olass jonalv: git is maybe not so good after all?
16:10 jonalv olass: I wonder if it's my eyes... but I don't know... we will see when it;s done..
16:11 egonw git-svn is not
16:11 olass jonalv: Now the eyes? Thought it was the hand that's bothering you...
16:11 egonw it's git scaled down to svn
16:11 olass :)
16:11 egonw seriously... git-svn sounds better than it is
16:11 olass ack
16:12 masak it's better than svn.
16:12 olass and better than cvs
16:12 olass and better than rsync
16:12 egonw is better than snail mail
16:12 egonw and better then tamtam
16:12 * olass is still using snail mail for versioning
16:13 egonw bbl
16:14 olass getting your snail mails?
16:14 olass yesterday's version?
16:18 olass SF is so slow... this is killing me...
16:18 olass *argh*
16:18 CIA-58 bioclipse: ospjuth * r9422 /bioclipse2/trunk/plugins/n​et.bioclipse.bibtexml.edit/ (85 files in 11 dirs): Added EMF edit code for bibtexml model.
16:18 * olass wants git
16:18 CIA-58 bioclipse: ospjuth * r9423 /bioclipse2/trunk/plugins/ne​t.bioclipse.bibtexml.tests/: Initial import.
16:19 masak olass: you can have it anytime you want. it's free.
16:20 olass no, comes with a cost
16:20 masak (gratis too, but I meant libre)
16:20 olass you have to spend time learning
16:20 masak olass: you had to for SVN, too.
16:20 olass time is precious
16:20 olass ...prrreciousss...
16:20 masak "FOSS is only free if your time is not worth anything" :P
16:21 olass FOSS?
16:21 masak Free/Open Source Software.
16:21 olass ah, true
16:22 CIA-58 bioclipse: ospjuth * r9424 /bioclipse2/trunk/plugins/ne​t.bioclipse.bibtexml.tests/ (35 files in 8 dirs): Added tests for bibtexml model.
16:25 egonw snail mail is OK
16:25 egonw bad I do not type so fast
16:26 egonw bad=but
16:26 egonw that's the limiting factor
16:27 masak egonw: http://steve-yegge.blogspot.com/2008/09/​programmings-dirtiest-little-secret.html
16:27 zarah masak's link is also http://tinyurl.com/6f9lsz
16:39 CIA-58 bioclipse: carl_masak * r9425 /bioclipse2/trunk/plugins/net.bioclip​se.scripting.ui/src/net/bioclipse/scr​ipting/ui/views/JsConsoleView.java:
16:39 CIA-58 bioclipse: [JsConsoleView] s/end of file/end of line/
16:39 CIA-58 bioclipse: The js console now gives an error message that makes for sense for the medium.
16:39 CIA-58 bioclipse: Fixes #113.
16:39 zarah bug #113 | http://tinyurl.com/5hey86
16:47 CIA-58 bioclipse: egonw * r9426 /bioclipse2/trunk/plugins/net.bioclipse.jmol/src​/net/bioclipse/jmol/actions/ExportHandler.java: Add .png when not ending in .png (fixes #580)
16:47 zarah bug #580 | http://tinyurl.com/cdmo5e
16:47 egonw dinner
16:47 egonw bbl
17:05 jonalv git-svn is rebuilding every good damn branch for me. It's gonna take like forever! :/
17:19 egonw olass: ping
17:19 egonw olass: what do I need to do to test the bibtexml plugin?
17:26 jonalv olass: that picked text that you where reffering to is printed long way inside Jmol internals... :(
17:39 olass egonw: nothing
17:39 olass egonw: it's just the model
17:39 olass what else is there?
17:39 egonw dunno...
17:39 olass :)
17:39 egonw edit suggested an editor
17:40 olass nope
17:40 olass that's editor
17:40 olass did not generate that
17:40 egonw ic
17:40 olass no use
17:40 egonw why not??
17:40 olass I want the model
17:40 egonw ic
17:40 olass what for?
17:40 egonw Speclipse would benefit much
17:40 egonw which now uses a plain test bibtex editor
17:40 olass have you any idea how it looks like?
17:40 egonw no
17:41 egonw generated .editor's are crap?
17:41 olass it's just an xml editor
17:41 olass well not crap
17:41 egonw ok, that sucks
17:41 olass but not user friendly
17:41 egonw EMF--
17:41 olass it's a GUI too
17:41 egonw ok, going to eat dessert now
17:41 olass :)
17:41 olass EMF++
17:41 olass you'll see the GUI
17:41 olass but it's just a stub
17:41 egonw ok, yes, please do
17:41 olass needs work to be good
17:41 egonw ok
17:41 olass ok will do
17:41 olass committing later
17:41 olass now: train
17:42 olass egonw: remember 20.00 with edrin
17:42 olass @tell egonw remember 20.00 with edrin
17:42 zarah Consider it noted.
17:42 olass bye
17:49 CIA-58 bioclipse: shk3 * r9427 /bioclipse2/trunk/plugins/ (5 files in 4 dirs): The switch workspace stuff works. I will send an email about it.
18:15 Juul joined #bioclipse
18:16 egonw hi Juul
18:16 zarah egonw: You have new messages. Write '/msg zarah @messages' to read them.
18:16 Juul hello
18:16 zarah saluton Juul
18:18 egonw Juul: you're Swedish? (have me met before?)
18:19 Juul egonw, danish, and no i don't think so :)
18:19 Juul using a swedish isp
18:19 egonw ic :)
18:19 egonw welcome
18:19 Juul thanks, i just did a channel search for "bio" on freenode
18:19 Juul seemed interesting
18:19 egonw yes, it is :)
18:19 Juul i'm just now reading about bioclipse
18:20 Juul you wouldn't happen to know what an "e-tag" is?
18:20 Juul in biotechnology, not IT
18:21 egonw no
18:22 Juul ah
18:49 edrin joined #bioclipse
19:00 edrin hi egonw
19:00 edrin egonw: can we postpone our meeting for 20 min?
19:03 egonw yes
19:05 olass joined #bioclipse
19:06 olass hi edrin
19:06 egonw olass: edrin is here but asked a 20 min delay
19:06 olass hi egonw
19:06 olass ok
19:06 olass fine with me
19:06 olass need to eat something
19:07 edrin :) me too
19:25 olass egonw: please explain ICDKManager.fragmentate(ICDKMOlecule).size() == 1
19:25 egonw to see if something is a salt, or a single molecule...
19:25 egonw fragmentate it...
19:25 egonw umm... maybe I should rename it to partition()
19:25 egonw anyway...
19:26 egonw in doing so, you get a list
19:26 egonw if the list has more than one element,
19:26 egonw then it is not a single molecule
19:26 egonw but, for example, a salt
19:27 olass and impossible to calculate descriptors for that?
19:27 olass I guess it should output a warning for that
19:27 olass good
19:29 egonw yes
19:29 egonw many descriptors are not even intended for charged molecules
19:29 egonw so, maybe warn about that too
19:34 olass how do I test for that?
19:34 olass charged mols?
19:34 olass is there a manager method for this?
19:34 egonw no
19:34 egonw in the current design that is not easy
19:35 egonw but your code can simply do:
19:35 edrin ok
19:35 edrin I am available now
19:35 olass edrin: you up?
19:35 egonw for (IAtom atom : container.atoms()) {
19:35 olass edrin: skype up
19:35 edrin starting
19:35 egonw totalCharge += atom.getFormalCharge() == null ? 0 : atom.getFormalCharge();
19:35 egonw }
19:35 edrin ok available
19:44 egonw http://pele.farmbio.uu.se/xmpp​-services/index.php/Main_Page
19:44 zarah egonw's link is also http://tinyurl.com/cevspc
19:45 edrin http://pele.farmbio.uu.se/xmpp-ser​vices/index.php/Main_Page_preview
19:45 zarah edrin's link is also http://tinyurl.com/dlqnhm
20:01 edrin egonw: preparing stuff now for you
20:01 egonw edrin: tack!
20:04 olass egonw: would it make sense to make a manager method that summed up all charges in all atoms?
20:04 olass or should I loop like you showed me?
20:05 egonw olass: I can make a total charge if you like
20:05 olass yes please
20:05 egonw but ICDKMolecule may not be a single molecule
20:05 egonw just keep that in mind
20:05 olass hmm
20:06 olass what will happen then?
20:06 olass an exception?
20:06 olass or should it report anyway?
20:06 egonw for example... for your salt, the total charge would be 0
20:07 olass right
20:07 olass charge would be 0 but fragments would be 2
20:08 egonw right
20:08 olass so the warnings together are useful
20:08 olass I'll add columns for this in the molecules tab
20:08 egonw olass++
20:08 olass with warning indications
20:08 olass I think it'll turn out quite well
20:08 olass but quite some work left... :)
20:09 * egonw already got 8 out of 18 points for his exam
20:09 olass oh right
20:09 olass now I remember
20:09 egonw olass: exam is too easy
20:09 olass told you
20:09 olass the level of education is low for pharmacists
20:09 olass AND
20:09 egonw it seems so
20:09 olass you get funding for every person that pass
20:09 olass hence
20:09 olass incitament to fail people is 0
20:10 egonw indeed
20:10 egonw mmm...
20:10 olass but in the long run it ruins teh standard
20:10 CIA-58 bioclipse: egonw * r9428 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Renamed method: partition is more accurate than fragment, which may suggest a reaction mechanism
20:10 * egonw will have to reconsider his cheminformatics course material
20:10 olass ok, gotta go now
20:10 olass cu tomorrow
20:10 egonw ok, bye
20:10 olass bye
20:23 edrin egon: I just created a binding for CML with xws4j-binding :/
20:24 edrin but i modified xws4j to also eat xsd files
20:34 egonw umm... what do you mean with that last?
20:34 egonw XML Schema == xsd, not?
20:36 edrin yes
20:37 egonw so, what did you modify then?
20:37 edrin egonw: i edited xws4j-binding, thus you can pass a .xsd file to it and it creates a binding with the file (from command line)
20:37 edrin (without any xmpp in between)
20:38 edrin i passed cml xsd file - and it worked!
20:39 edrin egonw: it seemed that it does work when passing the .xsd file
20:39 edrin thus maybe xmpp did something to the schema?
20:40 edrin egonw: i commited to svn
20:40 egonw ic...
20:41 egonw yeah, maybe...
20:41 egonw maybe the XMPP lib messes up encoding or so?
20:41 edrin yes, maybe
20:41 egonw or...
20:42 edrin but it worked for all other schematas :/
20:42 egonw maybe the schema is not properly wrapped in <out> ?
20:42 egonw true
20:42 egonw edrin: can you have the xws4j library save the content to file?
20:42 egonw then we can diff it against the original
20:43 edrin i can try...
20:43 edrin good idea
20:49 edrin js in bc does not work :/ restarting
20:57 CIA-58 bioclipse: egonw * r9429 /bioclipse2/trunk/plugins/ (3 files in 2 dirs): Added method to calculate the total formal charge
21:09 CIA-58 bioclipse: edrin_t * r9430 /xws/trunk/xws4j-binding/src​/net/bioclipse/xws/binding/ (BatchBinder.java BindingManager.java tools/Xsd2Class.java): now creating a binding by passing a .xsd file to it is possible.
21:21 edrin egonw: where can i get the current cml schema .xsd file?
21:23 edrin1 joined #bioclipse
21:24 egonw umm... mom
21:25 edrin1 egonw: i will try to extract the schema from the service and compare it...
21:25 edrin1 i tried creating binding with the old cml i still have here
21:25 egonw http://cdk.svn.sourceforge.net/viewvc​/cdk/cdk-xws/trunk/xws-qsar-services/​src/org/openscience/cdk/xws/schema/
21:25 zarah egonw's link is also http://tinyurl.com/dja33a
21:25 edrin1 ok
21:26 edrin1 egonw: I now need to play quake 3 live
21:27 CIA-58 bioclipse: ospjuth * r9431 /bioclipse2/trunk/plugins/net.bioclipse.bibtexml/ (.classpath .settings/ .settings/org.eclipse.jdt.core.prefs): Settings update.
21:29 CIA-58 bioclipse: ospjuth * r9432 /bioclipse2/trunk/plugins/​net.bioclipse.qsar.model/ (70 files in 9 dirs): Updated qsarmodel to import bibtexml and generated model for this. Did not manage to refactor out bibtex from generation so in same model. Not ideal but might have to be this way for now. At least it works.
21:29 egonw edrin1: :)
21:29 CIA-58 bioclipse: edrin_t * r9433 /bioclipse2/trunk/plugins/net.bioclipse.xws4j/ (7 files in 3 dirs): updated to current xws svn
21:48 edrin1 egonw: cml.xml it seemed to create binding for the schema in cml.xml properly
21:52 egonw ok
21:52 egonw let me know if you find more, and if I can do anything...
21:52 egonw going to bed now and sleep
21:52 edrin1 me too,
21:52 egonw got spend more than an hour on a blog item:
21:52 egonw http://chem-bla-ics.blogspot.com/2009/03/​nature-chemistry-improves-publishing.html
21:52 edrin1 will report what i find
21:52 zarah egonw's link is also http://tinyurl.com/dfvgon
21:52 egonw thanx
21:52 egonw cu later!
21:52 edrin1 cu

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